Align N-acetylornithine carbamoyltransferase (EC 2.1.3.9) (characterized)
to candidate 199472 SO0277 ornithine carbamoyltransferase (NCBI ptt file)
Query= BRENDA::Q8P8J2 (339 letters) >FitnessBrowser__MR1:199472 Length = 301 Score = 144 bits (363), Expect = 3e-39 Identities = 105/335 (31%), Positives = 161/335 (48%), Gaps = 40/335 (11%) Query: 3 LKHFLNTQDWSRAELDALLTQAALFKRN--KLGSELKGKSIALVFFNPSMRTRTSFELGA 60 +KHFL+ ++ ++ +L L+T A K N + L GKS+ ++F PS+RTR SF++G Sbjct: 1 MKHFLSIKELTQQQLLDLITLAKTIKANPAEYRHALDGKSVVMLFEKPSLRTRVSFDIGI 60 Query: 61 FQLGGHAVVLQPGKDAWPIEFNLGTVMDGDTEEHIAEVARVLGRYVDLIGVRAFPKFVDW 120 + GGH + L A LG E +A+ A L + D I R + Sbjct: 61 NKFGGHCLYLDQQNGA------LGK------RESVADFASNLSCWADAIVARTY------ 102 Query: 121 SKDREDQVLKSFAKYSPVPVIN-METITHPCQELAHALALQEHFGTPDLRGKKYVLTWTY 179 ++ A++ VPVIN + + HPCQ LA L L EHF YV Sbjct: 103 ----SHTTIEQLAEFGTVPVINALSDLYHPCQALADFLTLAEHFENISDVKLAYVGD--- 155 Query: 180 HPKPLNTAVANSALTIATRMGMDVTLLCPTPDYILDERYMDWAAQNVAES-GGSLQVSHD 238 V NS + A +G +T++CP + + Y+ Q +A GG + ++ D Sbjct: 156 -----GNNVTNSLMYCAAILGATMTVICPAGHF--PDGYVVAEVQELASRYGGKIVLTSD 208 Query: 239 IDSAYAGADVVYAKSWGALPFFGNWEPEKPIRDQYQHFIVDERKMALTNNGVFSHCLPLR 298 ID A G D +Y +W ++ G+ P I+D++ + V+ MA F HCLP Sbjct: 209 ID-AIEGHDAIYTDTWISM---GDPTPLAEIKDKFAPYQVNNALMAKAGAHFFMHCLPAH 264 Query: 299 RNVKATDAVMDSPNCIAIDEAENRLHVQKAIMAAL 333 R V+ TDAVMD + + +AENR+H Q A++ L Sbjct: 265 RGVEVTDAVMDGECSLILQQAENRMHAQNAVLVTL 299 Lambda K H 0.320 0.134 0.412 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 252 Number of extensions: 13 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 339 Length of database: 301 Length adjustment: 28 Effective length of query: 311 Effective length of database: 273 Effective search space: 84903 Effective search space used: 84903 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory